I am struggling to want using Socrates. (http://bioinf.wehi.edu.au/socrates/)
I looked up its web pages and followed the procedure written in it.
However, when I tried to run the second step called "realignment process", program show me warning message
and I suppose that this warning message might be affect my final results.
Below is my warning message.
./Socrates realignment filteredresults_long_sc_l25_q5_m5_i95.fastq.gz out3.bam --bowtie2_db filteredresults_long_sc_l25_q5_m5_i95.fasta
Bowtie2 alignment, DB=filteredresults_long_sc_l25_q5_m5_i95.fasta
115 reads; of these:
115 (100.00%) were unpaired; of these:
11 (9.57%) aligned 0 times
83 (72.17%) aligned exactly 1 time
21 (18.26%) aligned >1 times
90.43% overall alignment rate
Add anchor information into re-alignment BAM file
input BAM file: -
output BAM file: out3.bam
WARNING: 115 alignments with no matching reference chromosome name
in realignment BAM's sequence dictionary. Please ensure the same alignment indexes
are used for both raw read alignment and soft-clip realignment.
I think that Socrates was developed in 2014 and many people do not use it
,However, Is someone who already used it and got the final results,
Could you help me and advise for my problem?